Mercurial > repos > iuc > plink

comparison plink.xml @ 10:c7d38dcbf02d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
author iuc
date Sun, 19 Dec 2021 15:52:45 +0000
parents 303123b30425
children
comparison
equal deleted inserted replaced
9:303123b30425 10:c7d38dcbf02d
1 <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'> 1 <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'>
2 <macros> 2 <macros>
3 <token name='@TOOL_VERSION@'>1.9.b618</token> 3 <token name='@TOOL_VERSION@'>1.90b6.21</token>
4 <token name='@VERSION_SUFFIX@'>3</token> 4 <token name='@VERSION_SUFFIX@'>0</token>
5 <xml name='template_sanitizer'> 5 <xml name='template_sanitizer'>
6 <sanitizer> 6 <sanitizer>
7 <valid initial='default'> 7 <valid initial='default'>
8 <add value='#' /> 8 <add value='#' />
9 <add value='@' /> 9 <add value='@' />
35 <valid initial='string.ascii_letters + string.digits'> 35 <valid initial='string.ascii_letters + string.digits'>
36 <add value=' '/> 36 <add value=' '/>
37 </valid> 37 </valid>
38 </sanitizer> 38 </sanitizer>
39 </xml> 39 </xml>
40 <xml name="log_out_assert">
41 <output name="plink_log">
42 <assert_contents>
43 <has_text text="End time:"/>
44 </assert_contents>
45 </output>
46 </xml>
40 </macros> 47 </macros>
41 <xrefs> 48 <xrefs>
42 <xref type="bio.tools">plink</xref> 49 <xref type="bio.tools">plink</xref>
43 </xrefs> 50 </xrefs>
44 <requirements> 51 <requirements>
45 <requirement type='package' version='1.90b6.18'>plink</requirement> 52 <requirement type='package' version='@TOOL_VERSION@'>plink</requirement>
46 </requirements> 53 </requirements>
47 <command detect_errors='exit_code'><![CDATA[ 54 <command detect_errors='exit_code'><![CDATA[
48 55
49 ## Create Plink folder for any inputs 56 ## Create Plink folder for any inputs
50 mkdir ./plink_output 57 mkdir ./plink_output
53 60
54 ## If bmerge is set, create folder for merged files 61 ## If bmerge is set, create folder for merged files
55 #if $functions.func == 'data_manage': 62 #if $functions.func == 'data_manage':
56 #if $functions.bmerge.set == 'Yes': 63 #if $functions.bmerge.set == 'Yes':
57 && mkdir bmerge_files 64 && mkdir bmerge_files
58 && ln -s '$functions.bmerge.bed' bmerge_files/bmerge_input.bed 65 && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bed bmerge_files/bmerge_input.bed
59 && ln -s '$functions.bmerge.bim' bmerge_files/bmerge_input.bim 66 && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bim bmerge_files/bmerge_input.bim
60 && ln -s '$functions.bmerge.fam' bmerge_files/bmerge_input.fam 67 && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.fam bmerge_files/bmerge_input.fam
61 #end if 68 #end if
62 #end if 69 #end if
63 70
64 71
65 #if $inputs.inputs.filetype == 'bfile': 72 #if $inputs.inputs.filetype == 'bfile':
66 && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed 73 && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bed plink_input/plink_input.bed
67 && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim 74 && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bim plink_input/plink_input.bim
68 && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam 75 && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.fam plink_input/plink_input.fam
69 && plink --bfile plink_input/plink_input 76 && plink --bfile plink_input/plink_input
70 #elif $inputs.inputs.filetype == 'vcf': 77 #elif $inputs.inputs.filetype == 'vcf':
71 #if $inputs.inputs.input.is_of_type('bcf'): 78 #if $inputs.inputs.input.is_of_type('bcf'):
72 && plink --bcf '$inputs.inputs.input' 79 && plink --bcf '$inputs.inputs.input'
73 #else: 80 #else:
400 && mkdir assoc_out 407 && mkdir assoc_out
401 && mv ./plink_output/*asso* assoc_out 408 && mv ./plink_output/*asso* assoc_out
402 && find ./assoc_out/. -type f -exec mv {} {}.txt ';' 409 && find ./assoc_out/. -type f -exec mv {} {}.txt ';'
403 #end if 410 #end if
404 #end if 411 #end if
412 && mkdir '$plink_out.extra_files_path'
413 && cp plink_output/plink_output.bed '$plink_out.extra_files_path'/RgeneticsData.bed
414 && cp plink_output/plink_output.bim '$plink_out.extra_files_path'/RgeneticsData.bim
415 && cp plink_output/plink_output.fam '$plink_out.extra_files_path'/RgeneticsData.fam
405 ]]></command> 416 ]]></command>
406 <inputs> 417 <inputs>
407 <section name='inputs' title='Data inputs' expanded='true'> 418 <section name='inputs' title='Data inputs' expanded='true'>
408 <conditional name='inputs'> 419 <conditional name='inputs'>
409 <param name='filetype' type='select' label='Main input data type'> 420 <param name='filetype' type='select' label='Main input data type'>
410 <option value='bfile'>plink file</option> 421 <option value='bfile'>plink file</option>
411 <option value='vcf'>VCF input file</option> 422 <option value='vcf'>VCF input file</option>
412 </param> 423 </param>
413 <when value='bfile'> 424 <when value='bfile'>
414 <param format='pbed' name='bed' type='data' label='plink bed file'/> 425 <param format='pbed' name='bed' type='data' label='plink bed file'/>
415 <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/>
416 <param format='txt' name='fam' type='data' label='plink fam file'/>
417 </when> 426 </when>
418 <when value='vcf'> 427 <when value='vcf'>
419 <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/> 428 <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/>
420 </when> 429 </when>
421 </conditional> 430 </conditional>
669 <option value='No'>No</option> 678 <option value='No'>No</option>
670 <option value='Yes'>Yes</option> 679 <option value='Yes'>Yes</option>
671 </param> 680 </param>
672 <when value='No'/> 681 <when value='No'/>
673 <when value='Yes'> 682 <when value='Yes'>
674 <param format='binary' name='bed' type='data' label='plink bed file'/> 683 <param format='pbed' name='bed' type='data' label='plink bed file'/>
675 <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/>
676 <param format='tabular,tsv' name='fam' type='data' label='plink fam file'/>
677 </when> 684 </when>
678 </conditional> 685 </conditional>
679 <param name='recode' type='boolean' label='Recode' truevalue='--recode' falsevalue='' checked='false' help='Create a new text fileset, after applying sample/variant filters and other operations'/> 686 <param name='recode' type='boolean' label='Recode' truevalue='--recode' falsevalue='' checked='false' help='Create a new text fileset, after applying sample/variant filters and other operations'/>
680 <param format='tsv,tabular' name='flip' type='data' label='Flip DNA strand for SNPs' help='Given a file containing a list of SNPs with A/C/G/T alleles, --flip swaps A↔T and C↔G.' optional='true'/> 687 <param format='tsv,tabular' name='flip' type='data' label='Flip DNA strand for SNPs' help='Given a file containing a list of SNPs with A/C/G/T alleles, --flip swaps A↔T and C↔G.' optional='true'/>
681 <param name='template' type='text' label='Update Variant Info: Template String' help='Replaces missing IDs. The parameter taken by these flags is a special template string, with a @ where the chromosome code should go, and a # where the base-pair position belongs.'> 688 <param name='template' type='text' label='Update Variant Info: Template String' help='Replaces missing IDs. The parameter taken by these flags is a special template string, with a @ where the chromosome code should go, and a # where the base-pair position belongs.'>
800 <param name='window' type='integer' label='Window size in bp' value='50' help='Window size'/> 807 <param name='window' type='integer' label='Window size in bp' value='50' help='Window size'/>
801 <param name='step' type='integer' label='Step size (variant ct)' value='5'/> 808 <param name='step' type='integer' label='Step size (variant ct)' value='5'/>
802 <param name='r2' type='float' label='Unphased Hardcall r^2 Threshold' value='0.2' /> 809 <param name='r2' type='float' label='Unphased Hardcall r^2 Threshold' value='0.2' />
803 </when> 810 </when>
804 </conditional> 811 </conditional>
805
806 </when> 812 </when>
807 <when value='stratification'> 813 <when value='stratification'>
808 <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/> 814 <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/>
809 <conditional name='cluster'> 815 <conditional name='cluster'>
810 <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'> 816 <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'>
991 </when> --> 997 </when> -->
992 </conditional> 998 </conditional>
993 </inputs> 999 </inputs>
994 <outputs> 1000 <outputs>
995 <!--Main--> 1001 <!--Main-->
996 <collection name='plink_out' type='list' label='Plink main outputs'> 1002 <data name="plink_out" format="pbed"/>
997 <data name='plink_bed' format='pbed' from_work_dir='plink_output/plink_output.bed'/> 1003
998 <data name='plink_bim' format='tabular' from_work_dir='plink_output/plink_output.bim'/> 1004 <data name="plink_log" format='txt' from_work_dir='plink_output/plink_output.log' label='${tool.name} on ${on_string}: Log'/>
999 <data name='plink_fam' format='txt' from_work_dir='plink_output/plink_output.fam'/>
1000 <data name='plink_log' format='txt' from_work_dir='plink_output/plink_output.log'/>
1001 </collection>
1002 1005
1003 <!--Data Manage--> 1006 <!--Data Manage-->
1004 <data name='plink_ped' format='txt' from_work_dir='plink_output/plink_output.ped' label='${tool.name}: Recode ped'> 1007 <data name='plink_ped' format='txt' from_work_dir='plink_output/plink_output.ped' label='${tool.name} on ${on_string}: Recode ped'>
1005 <filter>functions['func'] == 'data_manage' and functions['recode']</filter> 1008 <filter>functions['func'] == 'data_manage' and functions['recode']</filter>
1006 </data> 1009 </data>
1007 <data name='plink_map' format='txt' from_work_dir='plink_output/plink_output.map' label='${tool.name}: Recode map'> 1010 <data name='plink_map' format='txt' from_work_dir='plink_output/plink_output.map' label='${tool.name} on ${on_string}: Recode map'>
1008 <filter>functions['func'] == 'data_manage' and functions['recode']</filter> 1011 <filter>functions['func'] == 'data_manage' and functions['recode']</filter>
1009 </data> 1012 </data>
1010 1013
1011 <!--Stats--> 1014 <!--Stats-->
1012 <data name='frequency' format='tabular' from_work_dir='plink_output/plink_output.frq' label='${tool.name}: freq out'> 1015 <data name='frequency' format='tabular' from_work_dir='plink_output/plink_output.frq' label='${tool.name} on ${on_string}: freq out'>
1013 <filter>functions['func'] == 'stats' and functions['freq']</filter> 1016 <filter>functions['func'] == 'stats' and functions['freq']</filter>
1014 </data> 1017 </data>
1015 <data name='hardy_out' format='tabular' from_work_dir='plink_output/plink_output.hwe' label='${tool.name}: Hardy-Weinberg equilibrium'> 1018 <data name='hardy_out' format='tabular' from_work_dir='plink_output/plink_output.hwe' label='${tool.name} on ${on_string}: Hardy-Weinberg equilibrium'>
1016 <filter>functions['func'] == 'stats' and functions['hardy']</filter> 1019 <filter>functions['func'] == 'stats' and functions['hardy']</filter>
1017 </data> 1020 </data>
1018 <data name='missing_1' format='tabular' from_work_dir='plink_output/plink_output.imiss' label='${tool.name}: imiss'> 1021 <data name='missing_1' format='tabular' from_work_dir='plink_output/plink_output.imiss' label='${tool.name} on ${on_string}: imiss'>
1019 <filter>functions['func'] == 'stats' and functions['missing']</filter> 1022 <filter>functions['func'] == 'stats' and functions['missing']</filter>
1020 </data> 1023 </data>
1021 <data name='missing_2' format='tabular' from_work_dir='plink_output/plink_output.lmiss' label='${tool.name}: lmiss'> 1024 <data name='missing_2' format='tabular' from_work_dir='plink_output/plink_output.lmiss' label='${tool.name} on ${on_string}: lmiss'>
1022 <filter>functions['func'] == 'stats' and functions['missing']</filter> 1025 <filter>functions['func'] == 'stats' and functions['missing']</filter>
1023 </data> 1026 </data>
1024 <data name='het' format='tabular' from_work_dir='plink_output/plink_output.het' label='${tool.name}: Het'> 1027 <data name='het' format='tabular' from_work_dir='plink_output/plink_output.het' label='${tool.name} on ${on_string}: Het'>
1025 <filter>functions['func'] == 'stats' and functions['het']</filter> 1028 <filter>functions['func'] == 'stats' and functions['het']</filter>
1026 </data> 1029 </data>
1027 <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name}: Sex check'> 1030 <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name} on ${on_string}: Sex check'>
1028 <filter>functions['func'] == 'stats' and functions['sex']['sex_stats']</filter> 1031 <filter>functions['func'] == 'stats' and functions['sex']['sex_stats']</filter>
1029 </data> 1032 </data>
1030 1033
1031 <!--Association--> 1034 <!--Association-->
1032 <!--Assoc --> 1035 <!--Assoc -->
1079 <data name='eigenvals' format='txt' from_work_dir='plink_output/plink_output.mds.eigvals' label='${tool.name}: Eigenvals'> 1082 <data name='eigenvals' format='txt' from_work_dir='plink_output/plink_output.mds.eigvals' label='${tool.name}: Eigenvals'>
1080 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['mds']['mds_scaling'] == 'Yes' and functions['cluster']['mds']['modifiers'] and 'eigvals' in functions['cluster']['mds']['modifiers']</filter> 1083 <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['mds']['mds_scaling'] == 'Yes' and functions['cluster']['mds']['modifiers'] and 'eigvals' in functions['cluster']['mds']['modifiers']</filter>
1081 </data> 1084 </data>
1082 </outputs> 1085 </outputs>
1083 <tests> 1086 <tests>
1084 <test expect_num_outputs='5'> 1087 <test expect_num_outputs='2'>
1085 <section name='inputs'> 1088 <section name='inputs'>
1086 <conditional name='inputs'> 1089 <conditional name='inputs'>
1087 <param name='filetype' value='bfile'/> 1090 <param name='filetype' value='bfile'/>
1088 <param name='bed' value='plink.bed'/> 1091 <param name='bed' value='' ftype="pbed">
1089 <param name='bim' value='plink.bim'/> 1092 <composite_data value="plink.bim"/>
1090 <param name='fam' value='plink.fam'/> 1093 <composite_data value="plink.bed"/>
1094 <composite_data value="plink.fam"/>
1095 </param>
1091 </conditional> 1096 </conditional>
1092 </section> 1097 </section>
1093 <conditional name='functions'> 1098 <conditional name='functions'>
1094 <param name='func' value='filtering'/> 1099 <param name='func' value='filtering'/>
1095 <conditional name='id_list'> 1100 <conditional name='id_list'>
1131 <param name='sex_select' value='--filter-cases'/> 1136 <param name='sex_select' value='--filter-cases'/>
1132 <param name='no_sex_select' value='--allow-no-sex'/> 1137 <param name='no_sex_select' value='--allow-no-sex'/>
1133 <param name='nonfounders' value='--nonfounders'/> 1138 <param name='nonfounders' value='--nonfounders'/>
1134 </conditional> 1139 </conditional>
1135 </conditional> 1140 </conditional>
1136 <output_collection name='plink_out' type='list'> 1141 <output name="plink_out">
1137 <element name='plink_bed' file='test1_out.bed' compare='sim_size'/> 1142 <extra_files type="file" name="RgeneticsData.bed" value="test1_out.bed" compare='sim_size'/>
1138 <element name='plink_bim' file='test1_out.bim'/> 1143 <extra_files type="file" name="RgeneticsData.bim" value="test1_out.bim"/>
1139 <element name='plink_fam' file='test1_out.fam'/> 1144 <extra_files type="file" name="RgeneticsData.fam" value="test1_out.fam"/>
1140 </output_collection> 1145 </output>
1146 <expand macro="log_out_assert"/>
1141 </test> 1147 </test>
1142 1148
1143 <test expect_num_outputs='7'> 1149 <test expect_num_outputs='4'>
1144 <section name='inputs'> 1150 <section name='inputs'>
1145 <conditional name='inputs'> 1151 <conditional name='inputs'>
1146 <param name='filetype' value='bfile'/> 1152 <param name='filetype' value='bfile'/>
1147 <param name='bed' value='plink.bed'/> 1153 <param name='bed' value='' ftype="pbed">
1148 <param name='bim' value='plink.bim'/> 1154 <composite_data value="plink.bim"/>
1149 <param name='fam' value='plink.fam'/> 1155 <composite_data value="plink.bed"/>
1156 <composite_data value="plink.fam"/>
1157 </param>
1150 </conditional> 1158 </conditional>
1151 </section> 1159 </section>
1152 <conditional name='functions'> 1160 <conditional name='functions'>
1153 <param name='func' value='data_manage'/> 1161 <param name='func' value='data_manage'/>
1154 <conditional name='bmerge'> 1162 <conditional name='bmerge'>
1155 <param name='set' value='Yes'/> 1163 <param name='set' value='Yes'/>
1156 <param name='bed' value='plink_2.bed'/> 1164 <param name='bed' value='' ftype="pbed">
1157 <param name='bim' value='plink_2.bim'/> 1165 <composite_data value="plink_2.bim"/>
1158 <param name='fam' value='plink_2.fam'/> 1166 <composite_data value="plink_2.bed"/>
1167 <composite_data value="plink_2.fam"/>
1168 </param>
1159 </conditional> 1169 </conditional>
1160 <param name='recode' value='--recode'/> 1170 <param name='recode' value='--recode'/>
1161 <param name='template' value='@asd#123'/> 1171 <param name='template' value='@asd#123'/>
1162 <param name='length' value='23'/> 1172 <param name='length' value='23'/>
1163 <conditional name='update_cols'> 1173 <conditional name='update_cols'>
1166 <param name='col_num' value='1'/> 1176 <param name='col_num' value='1'/>
1167 <param name='var_col' value='2'/> 1177 <param name='var_col' value='2'/>
1168 <param name='skip' value='a'/> 1178 <param name='skip' value='a'/>
1169 </conditional> 1179 </conditional>
1170 </conditional> 1180 </conditional>
1171 <output_collection name='plink_out' type='list'> 1181 <output name="plink_out">
1172 <element name='plink_bed' file='test2_out.bed' compare='sim_size'/> 1182 <extra_files type="file" name="RgeneticsData.bed" value="test2_out.bed" compare='sim_size'/>
1173 <element name='plink_bim' file='test2_out.bim'/> 1183 <extra_files type="file" name="RgeneticsData.bim" value="test2_out.bim"/>
1174 <element name='plink_fam' file='test2_out.fam'/> 1184 <extra_files type="file" name="RgeneticsData.fam" value="test2_out.fam"/>
1175 </output_collection> 1185 </output>
1186 <expand macro="log_out_assert"/>
1176 <output name='plink_ped' file='out.ped'/> 1187 <output name='plink_ped' file='out.ped'/>
1177 <output name='plink_map' file='out.map'/> 1188 <output name='plink_map' file='out.map'/>
1178 </test> 1189 </test>
1179 1190
1180 <test expect_num_outputs='5'> 1191 <test expect_num_outputs='2'>
1181 <section name='inputs'> 1192 <section name='inputs'>
1182 <conditional name='inputs'> 1193 <conditional name='inputs'>
1183 <param name='filetype' value='vcf'/> 1194 <param name='filetype' value='vcf'/>
1184 <param name='input' value='test.vcf'/> 1195 <param name='input' value='test.vcf'/>
1185 </conditional> 1196 </conditional>
1186 </section> 1197 </section>
1187 <output_collection name='plink_out' type='list'> 1198 <output name="plink_out">
1188 <element name='plink_bed' file='vcf_out.bed'/> 1199 <extra_files type="file" name="RgeneticsData.bed" value="vcf_out.bed" compare='sim_size'/>
1189 <element name='plink_bim' file='vcf_out.bim'/> 1200 <extra_files type="file" name="RgeneticsData.bim" value="vcf_out.bim"/>
1190 <element name='plink_fam' file='vcf_out.fam'/> 1201 <extra_files type="file" name="RgeneticsData.fam" value="vcf_out.fam"/>
1191 </output_collection> 1202 </output>
1203 <expand macro="log_out_assert"/>
1192 </test> 1204 </test>
1193 1205
1194 <test expect_num_outputs='11'> 1206 <test expect_num_outputs='8'>
1195 <section name='inputs'> 1207 <section name='inputs'>
1196 <conditional name='inputs'> 1208 <conditional name='inputs'>
1197 <param name='filetype' value='bfile'/> 1209 <param name='filetype' value='bfile'/>
1198 <param name='bed' value='plink.bed'/> 1210 <param name='bed' value='' ftype="pbed">
1199 <param name='bim' value='x_plink.bim'/> 1211 <composite_data value="x_plink.bim"/>
1200 <param name='fam' value='plink.fam'/> 1212 <composite_data value="plink.bed"/>
1213 <composite_data value="plink.fam"/>
1214 </param>
1201 </conditional> 1215 </conditional>
1202 </section> 1216 </section>
1203 <conditional name='functions'> 1217 <conditional name='functions'>
1204 <param name='func' value='stats'/> 1218 <param name='func' value='stats'/>
1205 <param name='freq' value='--freq'/> 1219 <param name='freq' value='--freq'/>
1215 <param name='female_max_obvs' value='10'/> 1229 <param name='female_max_obvs' value='10'/>
1216 <param name='male_min_obvs' value='200'/> 1230 <param name='male_min_obvs' value='200'/>
1217 </conditional> 1231 </conditional>
1218 </conditional> 1232 </conditional>
1219 </conditional> 1233 </conditional>
1220 <output_collection name='plink_out' type='list'> 1234 <output name="plink_out">
1221 <element name='plink_bed' file='stats.bed'/> 1235 <extra_files type="file" name="RgeneticsData.bed" value="stats.bed" compare='sim_size'/>
1222 <element name='plink_bim' file='stats.bim'/> 1236 <extra_files type="file" name="RgeneticsData.bim" value="stats.bim"/>
1223 <element name='plink_fam' file='stats.fam'/> 1237 <extra_files type="file" name="RgeneticsData.fam" value="stats.fam"/>
1224 <element name='plink_fam' file='stats.fam'/> 1238 </output>
1225 </output_collection> 1239 <expand macro="log_out_assert"/>
1226 <output name='frequency' file='out.freq'/> 1240 <output name='frequency' file='out.freq'/>
1227 <output name='hardy_out' file='out.hardy'/> 1241 <output name='hardy_out' file='out.hardy'/>
1228 <output name='missing_1' file='out.imiss'/> 1242 <output name='missing_1' file='out.imiss'/>
1229 <output name='missing_2' file='out.lmiss'/> 1243 <output name='missing_2' file='out.lmiss'/>
1230 <output name='het' file='out.het'/> 1244 <output name='het' file='out.het'/>
1231 <output name='sex_check' file='out.sexcheck'/> 1245 <output name='sex_check' file='out.sexcheck'/>
1232 </test> 1246 </test>
1233 1247
1234 <test expect_num_outputs='7'> 1248 <test expect_num_outputs='4'>
1235 <section name='inputs'> 1249 <section name='inputs'>
1236 <conditional name='inputs'> 1250 <conditional name='inputs'>
1237 <param name='filetype' value='bfile'/> 1251 <param name='filetype' value='bfile'/>
1238 <param name='bed' value='plink.bed'/> 1252 <param name='bed' value='' ftype="pbed">
1239 <param name='bim' value='plink.bim'/> 1253 <composite_data value="plink.bim"/>
1240 <param name='fam' value='plink.fam'/> 1254 <composite_data value="plink.bed"/>
1255 <composite_data value="plink.fam"/>
1256 </param>
1241 </conditional> 1257 </conditional>
1242 </section> 1258 </section>
1243 <conditional name='functions'> 1259 <conditional name='functions'>
1244 <param name='func' value='link'/> 1260 <param name='func' value='link'/>
1245 <conditional name='set_indep'> 1261 <conditional name='set_indep'>
1247 <param name='window' value='51'/> 1263 <param name='window' value='51'/>
1248 <param name='step' value='6'/> 1264 <param name='step' value='6'/>
1249 <param name='r2' value='0.3'/> 1265 <param name='r2' value='0.3'/>
1250 </conditional> 1266 </conditional>
1251 </conditional> 1267 </conditional>
1252 <output_collection name='plink_out' type='list'> 1268 <output name="plink_out">
1253 <element name='plink_bed' file='test5_out.bed' compare='sim_size'/> 1269 <extra_files type="file" name="RgeneticsData.bed" value="test5_out.bed" compare='sim_size'/>
1254 <element name='plink_bim' file='test5_out.bim'/> 1270 <extra_files type="file" name="RgeneticsData.bim" value="test5_out.bim"/>
1255 <element name='plink_fam' file='test5_out.fam'/> 1271 <extra_files type="file" name="RgeneticsData.fam" value="test5_out.fam"/>
1256 </output_collection> 1272 </output>
1273 <expand macro="log_out_assert"/>
1257 <output name='prune_in' file='plink.prune.in'/> 1274 <output name='prune_in' file='plink.prune.in'/>
1258 </test> 1275 </test>
1259 1276
1260 <test expect_num_outputs='10'> 1277 <test expect_num_outputs='7'>
1261 <section name='inputs'> 1278 <section name='inputs'>
1262 <conditional name='inputs'> 1279 <conditional name='inputs'>
1263 <param name='filetype' value='bfile'/> 1280 <param name='filetype' value='bfile'/>
1264 <param name='bed' value='plink.bed'/> 1281 <param name='bed' value='' ftype="pbed">
1265 <param name='bim' value='plink.bim'/> 1282 <composite_data value="plink.bim"/>
1266 <param name='fam' value='plink.fam'/> 1283 <composite_data value="plink.bed"/>
1284 <composite_data value="plink.fam"/>
1285 </param>
1267 </conditional> 1286 </conditional>
1268 </section> 1287 </section>
1269 <conditional name='functions'> 1288 <conditional name='functions'>
1270 <param name='func' value='stratification'/> 1289 <param name='func' value='stratification'/>
1271 <param name='read_genome' value='plink.genome'/> 1290 <param name='read_genome' value='plink.genome'/>
1277 <param name='dimensions' value='10'/> 1296 <param name='dimensions' value='10'/>
1278 <param name='modifiers' value='eigendecomp,eigvals'/> 1297 <param name='modifiers' value='eigendecomp,eigvals'/>
1279 </conditional> 1298 </conditional>
1280 </conditional> 1299 </conditional>
1281 </conditional> 1300 </conditional>
1282 <output_collection name='plink_out' type='list'> 1301 <output name="plink_out">
1283 <element name='plink_bed' file='test6_out.bed' compare='sim_size'/> 1302 <extra_files type="file" name="RgeneticsData.bed" value="test6_out.bed" compare='sim_size'/>
1284 <element name='plink_bim' file='test6_out.bim'/> 1303 <extra_files type="file" name="RgeneticsData.bim" value="test6_out.bim"/>
1285 <element name='plink_fam' file='test6_out.fam'/> 1304 <extra_files type="file" name="RgeneticsData.fam" value="test6_out.fam"/>
1286 </output_collection> 1305 </output>
1306 <expand macro="log_out_assert"/>
1287 <output name='mds' value='plink.mds' compare='sim_size'/> 1307 <output name='mds' value='plink.mds' compare='sim_size'/>
1288 <output name='cluster1' value='plink.cluster1' compare='sim_size'/> 1308 <output name='cluster1' value='plink.cluster1' compare='sim_size'/>
1289 <output name='cluster2' value='plink.cluster2' compare='sim_size'/> 1309 <output name='cluster2' value='plink.cluster2' compare='sim_size'/>
1290 <output name='cluster3' value='plink.cluster3' compare='sim_size'/> 1310 <output name='cluster3' value='plink.cluster3' compare='sim_size'/>
1291 <output name='eigenvals' value='plink.mds.eigenval' compare='sim_size'/> 1311 <output name='eigenvals' value='plink.mds.eigenval' compare='sim_size'/>
1292 </test> 1312 </test>
1293 1313
1294 <test expect_num_outputs='8'> 1314 <test expect_num_outputs='5'>
1295 <section name='inputs'> 1315 <section name='inputs'>
1296 <conditional name='inputs'> 1316 <conditional name='inputs'>
1297 <param name='filetype' value='bfile'/> 1317 <param name='filetype' value='bfile'/>
1298 <param name='bed' value='plink.bed'/> 1318 <param name='bed' value='' ftype="pbed">
1299 <param name='bim' value='plink.bim'/> 1319 <composite_data value="plink.bim"/>
1300 <param name='fam' value='plink.fam'/> 1320 <composite_data value="plink.bed"/>
1321 <composite_data value="plink.fam"/>
1322 </param>
1301 </conditional> 1323 </conditional>
1302 </section> 1324 </section>
1303 <conditional name='functions'> 1325 <conditional name='functions'>
1304 <param name='func' value='association'/> 1326 <param name='func' value='association'/>
1305 <conditional name='assoc'> 1327 <conditional name='assoc'>
1326 <param name='beta' value='beta'/> 1348 <param name='beta' value='beta'/>
1327 <param name='intercept' value='intercept'/> 1349 <param name='intercept' value='intercept'/>
1328 </conditional> 1350 </conditional>
1329 <param name='lambda' value='1.0'/> 1351 <param name='lambda' value='1.0'/>
1330 </conditional> 1352 </conditional>
1331 <output_collection name='plink_out' type='list'> 1353 <output name="plink_out">
1332 <element name='plink_bed' file='out.assoc.bed' compare='sim_size'/> 1354 <extra_files type="file" name="RgeneticsData.bed" value="out.assoc.bed" compare='sim_size'/>
1333 <element name='plink_bim' file='out.assoc.bim'/> 1355 <extra_files type="file" name="RgeneticsData.bim" value="out.assoc.bim"/>
1334 <element name='plink_fam' file='out.assoc.fam'/> 1356 <extra_files type="file" name="RgeneticsData.fam" value="out.assoc.fam"/>
1335 </output_collection> 1357 </output>
1358 <expand macro="log_out_assert"/>
1336 <output_collection name='assoc_outfiles' type='list' count='2'> 1359 <output_collection name='assoc_outfiles' type='list' count='2'>
1337 <element name='plink_output.assoc.fisher.mperm' value='out.assoc.fisher.mperm' compare='sim_size'/> 1360 <element name='plink_output.assoc.fisher.mperm' value='out.assoc.fisher.mperm' compare='sim_size'/>
1338 <element name='plink_output.assoc.fisher' value='out.assoc.fisher'/> 1361 <element name='plink_output.assoc.fisher' value='out.assoc.fisher'/>
1339 </output_collection> 1362 </output_collection>
1340 <output_collection name='adjust_outfiles' type='list' count='1'> 1363 <output_collection name='adjust_outfiles' type='list' count='1'>
1345 <element name='plink_output.assoc.logistic.adjusted' value='out.assoc.logistic.adjusted'/> 1368 <element name='plink_output.assoc.logistic.adjusted' value='out.assoc.logistic.adjusted'/>
1346 <element name='plink_output.assoc.logistic.perm' value='out.assoc.logistic.perm' compare='sim_size'/> 1369 <element name='plink_output.assoc.logistic.perm' value='out.assoc.logistic.perm' compare='sim_size'/>
1347 </output_collection> 1370 </output_collection>
1348 </test> 1371 </test>
1349 1372
1350 <test expect_num_outputs='6'> 1373 <test expect_num_outputs='3'>
1351 <section name='inputs'> 1374 <section name='inputs'>
1352 <conditional name='inputs'> 1375 <conditional name='inputs'>
1353 <param name='filetype' value='bfile'/> 1376 <param name='filetype' value='bfile'/>
1354 <param name='bed' value='plink.bed'/> 1377 <param name='bed' value='' ftype="pbed">
1355 <param name='bim' value='plink.bim'/> 1378 <composite_data value="plink.bim"/>
1356 <param name='fam' value='plink.fam'/> 1379 <composite_data value="plink.bed"/>
1380 <composite_data value="plink.fam"/>
1381 </param>
1357 </conditional> 1382 </conditional>
1358 </section> 1383 </section>
1359 <conditional name='functions'> 1384 <conditional name='functions'>
1360 <param name='func' value='ibd'/> 1385 <param name='func' value='ibd'/>
1361 <conditional name='genome'> 1386 <conditional name='genome'>
1363 <param name='min' value='0.1'/> 1388 <param name='min' value='0.1'/>
1364 <param name='max' value='0.9'/> 1389 <param name='max' value='0.9'/>
1365 <param name='modifiers' value='full,unbounded,nudge'/> 1390 <param name='modifiers' value='full,unbounded,nudge'/>
1366 </conditional> 1391 </conditional>
1367 </conditional> 1392 </conditional>
1393 <expand macro="log_out_assert"/>
1368 <output name='genome' file='out.genome'/> 1394 <output name='genome' file='out.genome'/>
1369 </test> 1395 </test>
1370 </tests> 1396 </tests>
1371 <help><![CDATA[ 1397 <help><![CDATA[
1372 PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 1398 PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.